A droplet digital PCR assay to detect Chinese rice-field eels rhabdovirus.

Chinese rice-field eels rhabdovirus (CrERV) causes haemorrhagic disease in Chinese rice-field eels (Monopterus albus), leading to significant mortality and economic losses. Sensitive detection of CrERV nucleic acids is essential to control the spread of this pathogen and to treat infected individuals. Herein, we developed an efficient and sensitive droplet digital PCR (ddPCR) method to rapidly detect and quantify CrERV. The ddPCR assay optimal conditions were an annealing temperature of 53°C, and primer and probe concentrations of 0.5 and 0.25 µM, respectively. The assay had a diagnostic sensitivity of 0.23 copies/µL, and was highly specific, showing no cross reactivity with other viruses (infectious haematopoietic necrosis virus, grass carp reovirus, spring viremia of carp virus, largemouth bass ranavirus, carp edema virus, Chinese giant salamander iridovirus, and white spot syndrome virus). Real-time quantitative PCR testing of 30 Chinese rice-field eels samples detected CrERV in 7 samples (23.3%), whereas ddPCR detected CrERV in 12 samples (40%), demonstrating its higher sensitivity. Thus, ddPCR represents an advanced method to absolutely quantify CrERV in infected fish with low virus concentrations, providing a valuable tool to manage the spread and impact of CrERV.

Low-voltage single-atom electron microscopy with carbon-based nanomaterials.

The properties of materials are strongly correlated with their atomic scale structures. Achieving a comprehensive understanding of the atomic-scale structure-property relationship requires advancements of imaging and spectroscopy techniques. Aberration-corrected scanning transmission electron microscopy (STEM) has seen rapid development over the past decades and is now routinely employed for atomic-scale characterization. However, quantitative STEM imaging and spectroscopy analysis at the single-atom level is challenging due to the extremely weak signals generated from individual atom, thus imposing stringent requirements for analysis sensitivity. This review discusses the development and application of low-voltage STEM techniques with single-atom sensitivity, primarily based on recent research presented on an invited talk at the 5th 2D23 SALVE Symposium, including annular dark-field (ADF) imaging, functional imaging and electron energy-loss spectroscopy (EELS) analysis. Carbon-based nanomaterials were chosen as model systems for demonstrating the capabilities of single-atom STEM imaging and EELS analysis, due to their structural stability under low accelerating voltages and their rich physical and chemical properties. Moreover, this review summarizes recent advancements and applications of low-voltage single-atom STEM imaging and spectroscopy in the study of functional materials and discusses prospects for future developments.

Analysis of the Ag M4,5 EELS edge to study silver nanoparticle corrosion.

Electron energy loss spectra collected from fresh and corroded silver nanoparticles are compared with those from a number of reference materials, focusing on the M4,5 edge. Chemical shifts and changes in the energy loss near edge structure (ELNES) are described and found to be sufficient to distinguish metallic silver from chemically oxidised silver. The measurements, in conjunction with electron energy loss spectrum imaging, are used to assess the mechanisms for atmospheric corrosion of silver nanoparticles. We unambiguously assign the corrosion product under atmospheric conditions to be silver sulphide, but show the reaction process to be distinctly inhomogeneous, producing a variety of types of corroded particles. LAY DESCRIPTION: >Here, we use analytical electron microscopy to track the corrosion of silver nanoparticles and present chemical maps of the corrosion products. We show clear spectroscopic differences between metallic and corroded silver using the M4,5 electron energy loss spectral feature, which is not commonly studied. Our study shows that corrosion is due to interactions with sulphur in the atmosphere; and the corrosion is not uniform, but appears to develop from specific points on the surface of the nanoparticles.

Development of a Modular Cryo-Transfer Station for the Side-Entry Transmission Electron Microscope†.

Cryo-transfer stations are essential tools in the field of cryo-electron microscopy, enabling the safe transfer of frozen vitreous samples between different stages of the workflow. However, existing cryo-transfer stations are typically configured for only the two most popular sample holder geometries and are not commercially available for all electron microscopes. Additionally, they are expensive and difficult to customize, which limits their accessibility and adaptability for research laboratories. Here, we present a new modular cryo-transfer station that addresses these limitations. The station is composed entirely of 3D-printed and off the shelf parts, allowing it to be reconfigured to a fit variety of microscopes and experimental protocols. We describe the design and construction of the station and report on the results of testing the cryo-transfer station, including its ability to maintain cryogenic temperatures and transfer frozen vitreous samples as demonstrated by vibrational spectroscopy. Our findings demonstrate that the cryo-transfer station performs comparably to existing commercial models, while offering greater accessibility and customizability. The design for the station is open source to encourage other groups to replicate and build on this development. We hope that this project will increase access to cryo-transfer stations for researchers in a variety of disciplines with nonstandard equipment.

Probing Defectivity Beneath the Hydrocarbon Blanket in 2D hBN Using TEM-EELS.

The controlled creation and manipulation of defects in 2D materials has become increasingly popular as a means to design and tune new material functionalities. However, defect characterization by direct atomic-scale imaging is often severely limited by surface contamination due to a blanket of hydrocarbons. Thus, analysis techniques that can characterize atomic-scale defects despite the contamination layer are advantageous. In this work, we take inspiration from X-ray absorption spectroscopy and use broad-beam electron energy loss spectroscopy (EELS) to characterize defect structures in 2D hexagonal boron nitride (hBN) based on averaged fine structure in the boron K-edge. Since EELS is performed in a transmission electron microscope (TEM), imaging can be performed in-situ to assess contamination levels and other factors such as tears in the fragile 2D sheets, which can affect the spectroscopic analysis. We demonstrate the TEM-EELS technique for 2D hBN samples irradiated with different ion types and doses, finding spectral signatures indicative of boron-oxygen bonding that can be used as a measure of sample defectiveness depending on the ion beam treatment. We propose that even in cases where surface contamination has been mitigated, the averaging-based TEM-EELS technique can be useful for efficient sample surveys to support atomically resolved EELS experiments.

Second world record for Barathronus roulei Nielsen, 2019 (Ophidiiformes, Bythitidae), from the Porcupine Bank (Northeast Atlantic).

Barathronus is a genus of blind cusk eels comprising 11 valid species. In this paper, we report the second specimen ever documented of Barathronus roulei (Bythitidae) obtained from the Porcupine Bank by R.V. Vizconde de Eza using a bottom trawl at a depth of 1349 m. Morphological description and illustrations, including a radiograph, are provided. In addition, three new sequences corresponding to three different genes, cytochrome c oxidase subunit I (COI)-DNA barcoding, 16S ribosomal RNA (16S), and recombination activating protein 1 (RAG1), have been added to the molecular repositories, representing the first sequences for the species.

Experimental evidence of magnetism in a 2D electron gas at the CoO/Co3O4 interface by employing EMCD.

In the present study we investigate the CoO/Co3O4 interface in order to determine its intriguing magnetic behavior, which can be utilized for tailoring magnetic properties, enabling spin transport, enhancing magnetic coupling, tuning device functionalities, and realizing miniaturized magnetic devices for various technological applications. We decipher the magnetic properties of the CoO/Co3O4 interface from first principles calculations using Wien2k and probe them experimentally by employing electron energy-loss magnetic chiral dichroism (EMCD), which is an electron-energy loss spectrometry (EELS) based technique in the transmission electron microscope (TEM). Both, theory and experiment, are in perfect agreement and result in a ferromagnetic 2D-electron gas of 5Å thickness directly at the interface.

Structure and Formation Mechanisms in Tantalum and Niobium Oxides in Superconducting Quantum Circuits.

Improving the qubit's lifetime (T1) is crucial for fault-tolerant quantum computing. Recent advancements have shown that replacing niobium (Nb) with tantalum (Ta) as the base metal significantly increases T1, likely due to a less lossy native surface oxide. However, understanding the formation mechanism and nature of both surface oxides is still limited. Using aberration-corrected transmission electron microscopy and electron energy loss spectroscopy, we found that Ta surface oxide has fewer suboxides than Nb oxide. We observed an abrupt oxidation state transition from Ta2O5 to Ta, as opposed to the gradual shift from Nb2O5, NbO2, and NbO to Nb, consistent with thermodynamic modeling. Additionally, amorphous Ta2O5 exhibits a closer-to-crystalline bonding nature than Nb2O5, potentially hindering H atomic diffusion toward the oxide/metal interface. Finally, we propose a loss mechanism arising from the transition between two states within the distorted octahedron in an amorphous structure, potentially causing two-level system loss. Our findings offer a deeper understanding of the differences between native amorphous Ta and Nb oxides, providing valuable insights for advancing superconducting qubits through surface oxide engineering.

Probing the Polarization of Low-Energy Excitations in 2D Materials from Atomic Crystals to Nanophotonic Arrays Using Momentum-Resolved Electron Energy Loss Spectroscopy.

Spectroscopies utilizing free electron beams as probes offer detailed information on the reciprocal-space excitations of 2D materials such as graphene and transition metal dichalcogenide monolayers. Yet, despite the attention paid to such quantum materials, less consideration has been given to the electron-beam characterization of 2D periodic nanostructures such as photonic crystals, metasurfaces, and plasmon arrays, which can exhibit the same lattice and excitation symmetries as their atomic analogues albeit at drastically different length, momentum, and energy scales. Because of their lack of covalent bonding and influence of retarded electromagnetic interactions, important physical distinctions arise that complicate interpretation of scattering signals. Here we present a fully-retarded theoretical framework for describing the inelastic scattering of wide-field electron beams from 2D materials and apply it to investigate the complementarity in sample excitation information gained in the measurement of a honeycomb plasmon array versus angle-resolved optical spectroscopy in comparison to single monolayer graphene.

Probing Correlation of Optical Emission and Defect Sites in Hexagonal Boron Nitride by High-Resolution STEM-EELS.

Optically bright emitters in hexagonal boron nitride (hBN) often acting as a source of a single-photon are mostly attributed to point-defect centers, featuring localized intra-bandgap electronic states. Although vacancies, anti-sites, and impurities have been proposed as candidates, the exact physical and chemical nature of most hBN single-photon emitters (SPEs) within the visible region are still up for debate. Combining site-specific high-angle annular dark-field imaging (HAADF) with electron energy loss spectroscopy (EELS), we resolve and identify a few carbon substitutions among neighboring hBN hexagons, all within the same sample region, from which typical defect emission is observed. Our experimental results are further supported by first-principles calculations, through which the stability and possible optical transitions of the proposed carbon-defect complex are assessed. The presented correlation between optical emission and defects provides valuable information toward the controlled creation of emitters in hBN, highlighting carbon complexes as another probable cause of its visible SPEs.

Singular and Nonsingular Transitions in the Infrared Plasmons of Nearly Touching Nanocube Dimers.

Narrow gaps between plasmon-supporting materials can confine infrared electromagnetic energy at the nanoscale, thus enabling applications in areas such as optical sensing. However, in nanoparticle dimers, the nature of the transition between touching (zero gap) and nearly nontouching (nonzero gap ≲15 nm) regimes is still a subject of debate. Here, we observe both singular and nonsingular transitions in infrared plasmons confined to dimers of fluorine-doped indium oxide nanocubes when moving from touching to nontouching configurations depending on the dimensionality of the contact region. Through spatially resolved electron energy-loss spectroscopy, we find a continuous spectral evolution of the lowest-order plasmon mode across the transition for finite touching areas, in excellent agreement with the simulations. This behavior challenges the widely accepted idea that a singular transition always emerges in the near-touching regime of plasmonic particle dimers. The apparent contradiction is resolved by theoretically examining different types of gap morphologies, revealing that the presence of a finite touching area renders the transition nonsingular, while one-dimensional and point-like contacts produce a singular behavior in which the lowest-order dipolar mode in the touching configuration, characterized by a net induced charge in each of the particles, becomes unphysical as soon as they are separated. Our results provide valuable insights into the nature of dimer plasmons in highly doped semiconductors.

Hidden Impurities Generate False Positives in Single Atom Catalyst Imaging.

Single-atom catalysts (SACs) are an emerging class of materials, leveraging maximum atom utilization and distinctive structural and electronic properties to bridge heterogeneous and homogeneous catalysis. Direct imaging methods, such as aberration-corrected high-angle annular dark-field scanning transmission electron microscopy, are commonly applied to confirm the atomic dispersion of active sites. However, interpretations of data from these techniques can be challenging due to simultaneous contributions to intensity from impurities introduced during synthesis processes, as well as any variation in position relative to the focal plane of the electron beam. To address this matter, this paper presents a comprehensive study on two representative SACs containing isolated nickel or copper atoms. Spectroscopic techniques, including X-ray absorption spectroscopy, were employed to prove the high metal dispersion of the catalytic atoms. Employing scanning transmission electron microscopy imaging combined with single-atom-sensitive electron energy loss spectroscopy, we scrutinized thin specimens of the catalysts to provide an unambiguous chemical identification of the observed single-atom species and thereby distinguish impurities from active sites at the single-atom level. Overall, the study underscores the complexity of SACs characterization and establishes the importance of the use of spectroscopy in tandem with imaging at atomic resolution to fully and reliably characterize single-atom catalysts.

Nanoscale mapping of residual stresses in Al 2024 alloys using correlative and multimodal scanning transmission electron microscopy.

A methodology for the mapping of residual stresses in metal alloys has been developed by analyzing an isotropic and homogeneous Al2024 alloy with scanning transmission electron microscopy (STEM), combined with diffraction (4DSTEM) and electron energy loss spectroscopy (STEM-EELS) techniques of TEM. The investigations on the alloy's microstructure and elemental distributions were also carried out with conventional dark-field STEM (DFSTEM) and X-ray energy dispersive (EDS) techniques, respectively. Using the STEM-EELS technique, the Young's modulus (YM) is mapped in the (001) plane of the Al alloy in the same regions where the residual strain maps are generated in [1‾ 00] and [010] directions by using 4DSTEM technique. The YM vs. residual strain plot for the Al 2024 alloy revealed that the value of YM decreased by about ∼ 7 % after the tensile residual strain reached 0.02 %. Whereas such a decrease in YM happens after the compressively residual strain reaches -0.015 %. The residual stress maps were also obtained in accordance with the Hooke's law i.e., by multiplying YM map with the corresponding residual strain maps.

Unveiling Enhanced PEC Water Oxidation: Morphology Tuning and Interfacial Phase Change in α-Fe2O3@K-OMS-2 Branched Core-Shell Nanoarrays.

A simple fabrication method that involves two steps of hydrothermal reaction has been demonstrated for the growth of α-Fe2O3@K-OMS-2 branched core-shell nanoarrays. Different reactant concentrations in the shell-forming step led to different morphologies in the resultant composites, denoted as 0.25 OC, 0.5 OC, and 1.0 OC. Both 0.25 OC and 0.5 OC formed perfect branched core-shell structures, with 0.5 OC possessing longer branches, which were observed by SEM and TEM. The core K-OMS-2 and shell α-Fe2O3 were confirmed by grazing incidence X-ray diffraction (GIXRD), EDS mapping, and atomic alignment from high-resolution STEM images. Further investigation with high-resolution HAADF-STEM, EELS, and XPS indicated the existence of an ultrathin layer of Mn3O4 sandwiched at the interface. All composite materials offered greatly enhanced photocurrent density at 1.23 VRHE, compared to the pristine Fe2O3 photoanode (0.33 mA/cm2), and sample 0.5 OC showed the highest photocurrent density of 2.81 mA/cm2. Photoelectrochemical (PEC) performance was evaluated for the samples by conducting linear sweep voltammetry (LSV), applied bias photo-to-current efficiency (ABPE), electrochemical impedance spectroscopy (EIS), incident-photo-to-current efficiency (IPCE), transient photocurrent responses, and stability tests. The charge separation and transfer efficiencies, together with the electrochemically active surface area, were also investigated. The significant enhancement in sample 0.5 OC is ascribed to the synergetic effect brought by the longer branches in the core-shell structure, the conductive K-OMS-2 core, and the formation of the Mn3O4 thin layer formed between the core and shell.

Momentum-resolved EELS and CL study on 1D-plasmonic crystal prepared by FIB method.

We investigate a one-dimensional plasmonic crystal (1D PlC) using momentum-resolved electron energy loss spectroscopy (EELS) and cathodoluminescence (CL) techniques, which are complementary in terms of available optical information. The PlC sample is fabricated from large aluminum grains through the focused ion beam (FIB) method. This approach allows curving nanostructures with high crystallinity, providing platforms for detailed analysis of plasmonic nanostructures using both EELS and CL. The momentum-resolved EELS visualizes dispersion curves outside the light cone, confirming the existence of the surface plasmon polaritons (SPP) and local modes, while the momentum-resolved CL mapping analysis identified these SPP and local modes. Such synergetic approach of two electron-beam techniques offers full insights into both radiative and non-radiative optical properties in plasmonic or photonic structures.

Microscopic chemical characterization of epoxy resin with scanning transmission electron microscopy - electron energy-loss spectroscopy.

The structural characterization of epoxy resins is essential to improve the understanding on their structure-property relationship for promising high-performance applications. Among all analytical techniques, scanning transmission electron microscopy-electron energy-loss spectroscopy (STEM-EELS) is a powerful tool for probing the chemical and structural information of various materials at a high spatial resolution. However, for sensitive materials, such as epoxy resins, the structural damage induced by electron-beam irradiation limits the spatial resolution in the STEM-EELS analysis. In this study, we demonstrated the extraction of the intrinsic features and structural characteristics of epoxy resins by STEM-EELS under electron doses below 1 e-/Å2 at room temperature. The reliability of the STEM-EELS analysis was confirmed by X-ray absorption spectroscopy and spectrum simulation as low- or non-damaged reference data. The investigation of the dependence of the epoxy resin on the electron dose and exposure time revealed the structural degradation associated with electron-beam irradiation, exploring the prospect of EELS for examining epoxy resin at low doses. Furthermore, the degradation mechanisms in the epoxy resin owing to electron-beam irradiation were revealed. These findings can promote the structural characterization of epoxy-resin-based composites and other soft materials.

Characteristic Plasmon Energies for 2D In2Se3 Phase Identification at Nanoscale.

Two-dimensional (2D) materials with competing polymorphs offer remarkable potential to switch the associated 2D functionalities for novel device applications. Probing their phase transition and competition mechanisms requires nanoscale characterization techniques that can sensitively detect the nucleation of secondary phases down to single-layer thickness. Here we demonstrate nanoscale phase identification on 2D In2Se3 polymorphs, utilizing their distinct plasmon energies that can be distinguished by electron energy-loss spectroscopy (EELS). The characteristic plasmon energies of In2Se3 polymorphs have been validated by first-principles calculations, and also been successfully applied to reveal phase transitions using in situ EELS. Correlating with in situ X-ray diffraction, we further derive a subtle difference in the valence electron density of In2Se3 polymorphs, consistent with their disparate electronic properties. The nanometer resolution and independence of orientation make plasmon-energy mapping a versatile technique for nanoscale phase identification on 2D materials.

Role of Curvature in Stabilizing Boron-Doped Nanocorrugated Graphene.

Boron-doped carbon nanostructures have attracted great interest recently because of their remarkable electrocatalytic performance comparable to or better than that of conventional metal catalysts. In a previous work (Carbon 123, 605 (2017)), we reported that along with significant performance improvement, B doping enhances the oxidation resistance of few-layer graphene (FLG) that provides increased structural stability for intermediate-temperature fuel-cell electrodes. In general, detailed characterization of the atomic and electronic structure transformations that occur in B-doped carbon nanostructures during fuel-cell operation is lacking. In this work, we use aberration-corrected scanning transmission electron microscopy, nanobeam electron diffraction, and electron energy-loss spectroscopy (EELS) to characterize the atomic and electronic structures of B-doped FLG before and after fuel-cell operation. These data point to the nanoscale corrugation of B-doped FLGs as the key factor responsible for increased stability and high corrosion resistance. The similarity of the 1s to π* and σ* transition features in the B K-edge EELS to those in B-doped carbon nanotubes provides an estimate for the curvature of nanocorrugation in B-FLG.

Probing Oxidation-Driven Amorphized Surfaces in a Ta(110) Film for Superconducting Qubit.

Recent advances in superconducting qubit technology have led to significant progress in quantum computing, but the challenge of achieving a long coherence time remains. Despite the excellent lifetime performance that tantalum (Ta) based qubits have demonstrated to date, the majority of superconducting qubit systems, including Ta-based qubits, are generally believed to have uncontrolled surface oxidation as the primary source of the two-level system loss in two-dimensional transmon qubits. Therefore, atomic-scale insight into the surface oxidation process is needed to make progress toward a practical quantum processor. In this study, the surface oxidation mechanism of native Ta films and its potential impact on the lifetime of superconducting qubits were investigated using advanced scanning transmission electron microscopy (STEM) techniques combined with density functional theory calculations. The results suggest an atomistic model of the oxidized Ta(110) surface, showing that oxygen atoms tend to penetrate the Ta surface and accumulate between the two outermost Ta atomic planes; oxygen accumulation at the level exceeding a 1:1 O/Ta ratio drives disordering and, eventually, the formation of an amorphous Ta2O5 phase. In addition, we discuss how the formation of a noninsulating ordered TaO1-δ (δ < 0.1) suboxide layer could further contribute to the losses of superconducting qubits. Subsurface oxidation leads to charge redistribution and electric polarization, potentially causing quasiparticle loss and decreased current-carrying capacity, thus affecting superconducting qubit coherence. The findings enhance the comprehension of the realistic factors that might influence the performance of superconducting qubits, thus providing valuable guidance for the development of future quantum computing hardware.

Observation of Sub-10 nm Transition Metal Dichalcogenide Nanocrystals in Rapidly Heated van der Waals Heterostructures.

Two-dimensional materials, such as transition metal dichalcogenides (TMDCs), have the potential to revolutionize the field of electronics and photonics due to their unique physical and structural properties. This research presents a novel method for synthesizing crystalline TMDCs crystals with <10 nm size using ultrafast migration of vacancies at elevated temperatures. Through in situ and ex situ processing and using atomic-level characterization techniques, we analyzed the shape, size, crystallinity, composition, and strain distribution of these nanocrystals. These nanocrystals exhibit electronic structure signatures that differ from the 2D bulk: i.e., uniform mono- and multilayers. Further, our in situ, vacuum-based synthesis technique allows observation and comparison of defect and phase evolution in these crystals formed under van der Waals heterostructure confinement versus unconfined conditions. Overall, this research demonstrates a solid-state route to synthesizing uniform nanocrystals of TMDCs and lays the foundation for materials science in confined 2D spaces under extreme conditions.